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Commit Graph
973 Commits
Author SHA1 Message Date
John Davis 2de79dd7d1 Add default task routes to config schema 2022-10-14 19:28:17 -04:00
John Davis 71829ae6af Add more details to setting db engine options to config schema 2022-10-14 13:18:35 -04:00
mahendrapaipuri c0002c1ffb Update authentication documentation with an example on how to use request object in auth flows 2022-10-14 09:46:59 +02:00
Nicola Soranzo 6069023d86 Merge pull request #14740 from bernt-matthias/topic/doc-security-datatables 
Extend security docs
 2022-10-13 14:29:52 +01:00
M BerntandMarius van den Beek ffc26d5ddd Update doc/source/admin/security.md 
Co-authored-by: Marius van den Beek <m.vandenbeek@gmail.com>
 2022-10-13 13:53:06 +02:00
Nicola Soranzo a81d680cca Merge branch 'release_22.05' into dev 2022-10-11 21:34:31 +01:00
Dannon Baker c8659d1d4a Add toolbox_auto_sort config option, expose in config manager. 2022-10-06 22:20:06 -04:00
M BerntandNicola Soranzo e8adc13324 Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-09-30 22:38:49 +02:00
M Bernt 37594348f9 Update doc/source/admin/security.md 2022-09-30 19:00:54 +02:00
John Davis 06744d4d0f Document use of release tags in manage_db.sh 2022-09-30 10:42:01 -04:00
Matthias Bernt eddd8e89a6 extend security docs 
by adding data referred by data tables
 2022-09-30 14:33:40 +02:00
John Davis 8538ab7fcb Fix same error in sample code in the rst doc file 2022-09-29 12:23:28 -04:00
John Davis 84f22bac77 Add db migration documentation to docs 2022-09-27 15:03:12 -04:00
John Davis 5a748bb867 Display 'Config Options' as subheading of 'Galaxy Configuration' 
This corrects a (supposedly) typo that prevented this to be displayed as
a subheading on this page: https://docs.galaxyproject.org/en/master/admin/index.html
 2022-09-27 15:03:03 -04:00
Sveinung Gundersen 4ec8c4654e Added info on galaxy.yml config 2022-09-23 17:54:01 +02:00
Sveinung Gundersen 89bf7b1e52 Adding documentation and example nginx config to allow path-based interactive tools 2022-09-23 17:19:31 +02:00
Nicola Soranzo e08deef224 Merge pull request #14592 from nsoranzo/misc_fixes_202209 
Misc fixes 202209
 2022-09-09 21:34:38 +01:00
Nicola Soranzo 157d9647ea Update docs on adding Python dependencies 
to use Wheelforge instead of Starforge.
 2022-09-09 17:26:30 +01:00
Nicola Soranzo 404da60afa Fix Tool Shed link 2022-09-09 17:20:24 +01:00
Nicola Soranzo cb012c7fb2 Merge branch 'release_22.05' into dev 2022-09-09 17:14:20 +01:00
Nicola Soranzo d8986239a1 Merge branch 'release_22.01' into release_22.05 2022-09-09 17:12:29 +01:00
Marius van den BeekandNicola Soranzo b05462a188 Add sbin to PATH 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-09-09 13:06:35 +02:00
mvdbeek 0256b34b34 Include /bin in sample systemd unit path 2022-09-09 12:52:05 +02:00
Dannon c7a275b13c Merge pull request #14570 from guerler/logout_url 
Add config option for post logout redirect url
 2022-09-07 08:00:33 -04:00
guerler 8350ff212e Add post logout url to configuration 2022-09-05 14:12:50 -04:00
Nicola Soranzo 0df5c9a5fb Updates for Poetry 1.2.0 
Also:
- Export only dev requirements to `lib/galaxy/dependencies/dev-requirements.txt` .
- Packages don't have a `requirements.txt` file.
 2022-09-05 17:23:18 +01:00
John Chilton 52d982bf74 Merge pull request #14558 from jdavcs/dev_schema_rename_option_ref 
Fix reference to config option in schema
 2022-09-02 14:39:42 -04:00
Nicola Soranzo e7d7c62de6 Merge branch 'release_22.05' into dev 2022-09-02 19:28:55 +01:00
Nate Coraor 86e42b5483 Update Gravity to 0.13.4 and document setting env vars on dynamic 
handlers.
 2022-09-01 10:40:54 -04:00
John Davis 241647c1f1 Run make config-rebuild 2022-08-31 18:08:26 -04:00
mvdbeek 2e22b9e1f8 Merge branch 'release_22.05' into dev 2022-08-22 19:17:35 +02:00
Nicola Soranzo 4fcbe80268 Doc fixes 2022-08-19 18:33:20 +01:00
qiagu 419b6835d5 Reword dependencies in Batch job runner doc 2022-08-18 12:42:39 -07:00
Qiang GuandNuwan Goonasekera 92ec7c60b1 Update doc/source/admin/cluster.md 
Co-authored-by: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
 2022-08-18 12:42:39 -07:00
Qiang GuandNuwan Goonasekera 049a9ee1d8 Update doc/source/admin/cluster.md 
Co-authored-by: Nuwan Goonasekera <2070605+nuwang@users.noreply.github.com>
 2022-08-18 12:42:39 -07:00
qiagu ddb011b698 Add admin doc for aws batch runner 2022-08-18 12:42:38 -07:00
Nate Coraor 4151f176bf Merge remote-tracking branch 'upstream/release_22.05' into dev 2022-08-17 16:37:02 -04:00
Marius van den Beek cd94ccb6c5 Merge pull request #14457 from natefoo/log-rotation 
[22.05] Add log rotation options and update logging documentation
 2022-08-17 19:24:07 +02:00
Nicola Soranzo 3378348d5e Merge branch 'release_22.05' into dev 2022-08-17 01:07:02 +01:00
Nicola Soranzo 961472cfff Merge branch 'release_22.01' into release_22.05 2022-08-16 23:25:42 +01:00
Nate Coraor 3522fd3a49 Add log rotation options and update logging documentation 2022-08-15 20:54:02 -04:00
Nicola Soranzo 69defb7a20 Doc fixes 2022-08-15 19:15:02 +01:00
Nicola Soranzo 575a1d8358 Merge pull request #14430 from bernt-matthias/unlink-job-template 
Deprecate `cluster_files_directory` and store DRMAA job template and PBS shell, error and out files in job working directory
 2022-08-13 01:00:10 +01:00
Dannon Baker 3112181f3e Merge remote-tracking branch 'upstream/release_22.05' into dev 2022-08-12 13:18:53 -04:00
Matthias Bernt b81b2f827e remove more leftover references to cluster_files_directory 2022-08-12 16:07:35 +02:00
mvdbeek 728ceebc8a Fix nested archive unzipping on windows 
We need the directory markers in order for the default windows zip
utility to be able to extract the archives. Also requires
https://github.com/evanmiller/mod_zip/commit/51cf45d3e9f51e02224af017b235d1d30fbf28fb
or newer on the mod_zip side.
 2022-08-10 17:33:29 +02:00
mvdbeek a351bd1ce9 Merge branch 'release_22.05' into dev 2022-08-09 15:12:15 +02:00
Cameron Hyde ffb9b34d89 Update config schema descriptions for tool search 2022-07-28 17:32:32 -05:00
Cameron Hyde 2ca6e7353b Add new config params for tool search 2022-07-28 17:29:58 -05:00
M BerntandNicola Soranzo ed5bdcefec Apply suggestions from code review 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-07-04 14:27:29 +02:00